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Utilizing Ancient DNA at GedMatch

It has been a wonderful week for those of us following ancient DNA full genome sequencing, because now we can compare our own results to those of the ancient people found whose DNA has been fully sequenced, including one Native American.

Felix Chandrakumar has uploaded the autosomal files of five ancient DNA specimens that have been fully sequenced to GedMatch. Thanks Felix.

When news of these sequences first hit the academic presses, I was wishing for a way to compare our genomes – and now my wish has come true.

Utilizing GedMatch’s compare one to all function, I ran all of the sequences individually and found, surprisingly, that there are, in some cases, matches to contemporary people today. I dropped the cM measure to 1 for both autosomal and X.

Please note that because these are ancient DNA sequences, they will all have some segments missing and none can be expected to be entirely complete. Still, these sequences are far better than nothing.

Thirty-nine matches with segments as large at 3.8. One group of matches appears to be a family. One of these matches is my cousin’s wife. That should lead to some interesting conversation around the table this holiday season! All of these matches, except 1, are on the X chromosome. This must be a function of these segments being passed intact for many generations.

I wrote about some unusual properties of X chromosomal inheritance and this seems to confirm that tendency in the X chromosome, or the matching thresholds are different at GedMatch for the X.

Two matches, one to yet another ancient entry and one to a contemporary individual on the X chromosome.

But now, for the fun part.

My Comparison

Before I start this section, I want to take a moment to remind everyone just how old these ancient segments are.

Anzick – about 12,500 years old

Paleo-Eskimo – about 4,000 years old

Altai Neanderthal – about 50,000 years old

Russian Caucasus Neanderthal – about 29,000 years old

Denisova – about 30,000 years old

In essence, the only way for these segments to survive intact to today would have been for them to enter the population of certain groups, as a whole, to be present in all of the members of that group, so that segment would no longer be divided and would be passed intact for many generation, until that group interbred with another group who did not carry that segment. This is exactly what we see in endogamous populations today, such as the Askenazi Jewish population who is believed, based on their common shared DNA, to have descended from about 350 ancestors about 700 years ago. Their descendants today number in the millions.

So, let’s see what we find.

I compared by own kit at GedMatch utilizing the one to one comparison feature, beginning with 500 SNPs and 1cM, dropping the SNP values to 400, then 300, then 200, until I obtained a match of some sort, if I obtained a match at all.

Typically in genetic genealogy, we’re looking for genealogy matches, so the default matching thresholds are set relatively high. In this case, I’m looking for deep ancestral connections, if they exist, so I was intentionally forcing the thresholds low. I’m particularly interested in the Anzick comparison, in light of my Native American and First Nations heritage.

IBS means that the genealogy connection cannot be found and the IBS match can be a function of coming from a common population at some time in the past, or it can be a match by convergence, meaning that your DNA just happened to mutate to the same state as someone else’s. If this is the case, then you wouldn’t expect to see multiple segments matching the same person and you would expect the matching segments to be quite short. The chances of hundreds of SNPs just happening to align becomes increasingly unlikely the longer the matching SNP run.

So, having said that, here are my match results.

Anzick

I had 2 matches at 400 SNPs, several at 300 and an entire list at 200, shown below.

Chr

Start Location

End Location

Centimorgans (cM)

SNPs

1

6769350

7734985

1.7

232

1

26552555

29390880

1.9

264

1

31145273

33730360

2.7

300

1

55655110

57069976

1.9

204

1

71908934

76517614

2.8

265

1

164064635

165878596

2.8

264

1

167817718

171330902

3.3

466

1

186083870

192208998

4.2

250

2

98606363

100815734

1.4

256

2

171132725

173388331

2.0

229

2

218855489

220373983

2.5

261

3

128892631

131141396

1.7

263

3

141794591

143848459

2.5

207

4

1767539

3571907

2.7

235

4

70345811

73405268

2.5

223

5

2340730

2982499

2.3

200

5

55899022

57881001

2.3

231

5

132734528

134538202

1.9

275

5

137986213

140659207

1.7

241

6

34390761

36370969

1.8

293

8

17594903

18464321

1.9

200

8

23758017

25732105

1.7

240

8

109589884

115297391

1.9

203

9

122177526

124032492

1.6

229

10

101195132

102661955

1.2

264

10

103040561

105596277

1.3

304

10

106135611

108371247

1.5

226

12

38689229

41184500

1.6

247

13

58543514

60988948

1.6

220

13

94528801

95252127

1.0

277

14

60929984

62997711

1.8

255

14

63724184

65357663

1.7

201

14

72345879

74206753

1.7

263

15

36850933

38329491

2.7

238

16

1631282

2985328

2.5

273

16

11917282

13220406

3.7

276

16

15619825

17324720

3.1

305

16

29085336

31390250

1.3

263

16

51215026

52902771

3.4

224

17

52582669

56643678

4.7

438

19

11527683

13235913

1.7

203

19

15613137

16316773

1.2

204

19

46195917

49338412

3.3

397

20

17126434

18288231

2.1

225

21

35367409

36969215

4.1

254

21

42399499

42951171

1.6

233

22

33988022

35626259

5.0

289

In my case, I’m particularly fortunate, because my mother tested her DNA as well. By process of elimination, I can figure out which of my matches are through her, and then by inference, which are through my father or are truly IBS by convergence.

I carry Native heritage on both sides, but my mother’s is proven to specific Native ancestors where my father’s is only proven to certain lines and not yet confirmed through genealogy records to specific ancestors.

Because I had so many matches, quite to my surprise, I also compared my mother’s DNA to the Anzick sample, combined the two results and put them in a common spreadsheet, shown below. White are my matches. Pink are Mom’s matches, and the green markers are on the segments where we both match the Anzick sample, confirming that my match is indeed through mother.

We’ll work with this information more in a few minutes.

Paleo

At 200 SNP level, 2 segments.

1

26535949

27884441

1.1

258

2

127654021

128768822

1.2

228

My mother matches on 9 segments, but neither of the two above, so they are either from my father’s side or truly IBS by convergence.

Altai Neanderthal

Russian Neanderthal

Neither my mother nor I have any matches at 100SNPs and 1cM.

Denisovan

I have one match.

Chr

Start Location

End Location

Centimorgans (cM)

SNPs

4

8782230

9610959

1.2

100

My mother matches 2 segments at 100 SNPs but neither match is the same as my segment.

Matching to Ancestral Lines

I’ve been mapping my DNA to specific ancestors utilizing the genealogy information of matches and triangulation for some time. This consists of finding common ancestors with your matches. Finding one person who matches you and maps to a common ancestor on a particular segment consists of a hint. Finding two that share the same ancestral line and match you and each other on the same segment is confirmation – hence, the three of you triangulate. More than three is extra gravy:)

I have also recorded other relevant information in my matches file, like the GedMatch Native chromosomal comparisons when I wrote “The Autosomal Me” series about hunting for my Native chromosomal segments.

So, after looking at the information above, it occurred to me that I should add this ancestral match information to my matches spreadsheet, just for fun, if nothing else.

I added these matches, noted the source as GedMatch and then sorted the results, anxious to see what we might find. Would at least one of these segments fall into the proven Native segments or the matches to people who also descend from those lines?

What I found was both astonishing and confusing….and true to form to genealogy, introduced new questions.

I have extracted relevant matching groups from my spreadsheet and will discuss them and why they are relevant. You can click on any of the images to see a larger image.

This first set of matches is intensely interesting, and equally as confusing.

First, these matches are to both me and mother, so they are confirmed through my mother’s lines. In case anyone notices, yes, I did switch my mother’s line color to white and mine to pink to be consistent with my master match spreadsheet coloration.

Second, both mother and I match the Anzick line on the matches I’ve utilized as examples.

Third, both 23andMe and Dr. Doug McDonald confirmed the segments in red as Native which includes the entire Anzick segment.

Fourth, utilizing the Gedmatch admixture tools, mother and I had this range in common. I described this technique in “The Autosomal Me” series.

Fifth, these segments show up for two distinct genealogy lines that do not intersect until my grandparents, the Johann Michael Miller line AND the Acadian Lore line.

Sixth, the Acadian Lore line is the line with proven Native ancestors.

Seventh, the Miller line has no Native ancestors and only one opportunity for a Native ancestor, which is the unknown wife of Philip Jacob Miller who married about 1750 to a women rumored to be Magdalena Rochette, but research shows absolutely no source for that information, nor any Rochette family anyplace in any proximity in the same or surrounding counties to the Miller family. The Miller’s were Brethren. Furthermore, there is no oral history of a Native ancestor in this line, but there have been other hints along the way, such as the matching segments of some of the “cousins” who show as Native as well.

Eighth, this makes my head hurt, because this looks, for all the world, like Philip Jacob Miller who was living in Bedford County, PA when he married about 1750 may have married someone related to the Acadian lines who had intermarried with the Micmac. While this is certainly possible, it’s not a possibility I would ever have suspected.

Let’s see what else the matches show.

In this matching segment Mom and I both match Emma, who descends from Marie, a MicMac woman. Mom’s Anzik match is part of this same segment.

In this matching segment, Mom and I both match cousin Denny who descends from the Lore line who is Acadian and confirmed to have MicMac ancestry. Mom’s Anzik segments all fit in this range as well.

In this matching segment, cousin Herbie’s match to Mom and I falls inside the Anzick segments of both Mom and I.

More matching to the proven Miller line.

This last grouping with Mom is equally as confusing at the first. Mom and I both match cousin Denny on the Lore side, proven Acadian.

Mom and I both match the Miller side too, and the Anzik for both of us falls dead center in these matches.

There are more, several more matches, that also indicate these same families, but I’m not including them because they don’t add anything not shown in these examples. Interestingly enough, there are no pointers to other families, so this isn’t something random. Furthermore, on my father’s side, as frustrating as it is, here are no Anzick matches that correlate with proven family lines. ARGGHHHHHH……

On matches that I don’t share with mother, there is one of particular interest.

You’ll notice that the Anzik and the Paleo-Greenland samples match each other, as well as me. This is my match, and by inference, not through mother. Unfortunately, the other people in this match group don’t know their ancestors or we can’t identify a common ancestor.

Given the genetic genealogy gold standard of checking to see if your autosomal matches match each other, I went back to GedMatch to see if the Paleo-Greenland kit matched the Clovis Anzik kit on this segment, and indeed, they do, plus many more segments as well. So, at some time, in some place, the ancestors of these two people separated by thousands of miles were related to each other. Their common ancestor would have either been in Asia or in the Northern part of Canada if the Paleo people from Greenland entered from that direction.

Regardless, it’s interesting, very interesting.

What Have I Learned?

Always do experiments. You never know what you’ll find.

I’m much more closely related to the Anzick individual than I am to the others. This isn’t surprising given my Native heritage along with the endogamous culture of the Acadians.

My relationship level to these ancient people is as follows:

Lived Years Ago

Relatedness

Comments

Montana Anzick

12,500

107.4cM at 200 SNP level

Confirmed to Lore (Acadian) and Miller, but not other lines

Greenland Paleo

4,000

2.3cM at 200 SNP level

No family line matches, does match to Anzick in one location

Altai Neanderthal

50,000

2.1cM at 200 SNP level

No family line matches

Russian Neanderthal

29,000

0

Denisovan

30,000

1.2cM at 200 SNP

No family line matches

The Lores and the Millers

Looking further at the Lore and Miller lines, there are only two options for how these matching segments could have occurred. There are too many for them all to be convergence, so we’ll have to assume that they are indeed because we shared a common population at some time and place.

The nature of how small the segments are testify that this is not a relatively recent common ancestor, but how “unrecent” is open to debate. Given that Neanderthal and Denisovan ancient segments are found in all Europeans today, it’s certainly possible for these segments to be passed intact, even after thousands of years.

The confirmations to the Lore line come through proven Lore cousins and also through other proven Acadian non-specific matches. This means that the Acadian population is highly endogamous and when I find an Acadian match, it often means that I’m related through many ancestors many times. This, of course, increases the opportunity for the DNA to be passed forward, and decreases the opportunity for it to be lost in transmission, but it also complicates the genealogy greatly and makes determining which ancestor the DNA segment came from almost impossible.

However, I think we are safe to say the segments are from the Acadian population, although my assumption would be that they are from the Native Ancestors and not the French, given the high number of Anzick matches, Anzick being proven to be Native. Having said that, that assumption may not be entirely correct.

The Miller line is relatively well documented and entirely from Germany/Switzerland, immigrating in the early 1700s, with the exception of the one unknown wife in the first generation married in the US. Further examination would have to be done to discover if any of the matches came through Johann Michael Miller’s sons other than Philip Jacob Miller, my ancestor. There are only three confirmed children, all sons. If this segment shows up in Johann Michael Miller’s line not associated with son Philip Jacob Miller, then we would confirm that indeed the segment came from Europe and not a previously unknown Native or mixed wife of Philip Jacob.

Bottom Line

So, what’s the bottom line here? I know far more than I did. The information confirms, yet again, the Acadian Native lines, but it introduces difficult questions about the Miller line. I have even more tantalizing questions for which I have no answers today, but I tell you what, I wouldn’t trade this journey along the genetic pathway with all of its unexpected bumps, rocks, slippery slopes and crevices for anything!! That’s why it’s called an adventure!

I am working on NA – it was a promise to granny. She lived to be 100 years 3 mths 22 days. But I was not able to give her any answers before her passing. So mom and I are working together. Mom is a Buchanan descendant in TN- and was told she is related to Sarah Sally Ridley and her mom was Elizabeth Marie Weatherford- which I have been told she was Shawano-Chalaiwa-Nanticoke-Metis. Paper trails are difficult..

So I’m interested if all Mexican Americans have some ties to the Natives found in California. My World 22 admixture says I’m close to the Serrano people. I don’t have paper trails cause my family never kept anything. I’ve only gotten to my great grandparents and that is it.

Yes, Native people all descend from a very small population who had no one but others to intermarry with except others descended from the same population for thousands of years. So yes, they are related and connected.

First of all I would like to ask you to be indulgent with my English because I’m a french speaker . The results that I received with this tool made me confused, I explain. I am mostly of African ancestry, and depending on which company I tested I have 7,8, 9 or 12% of European ancestry, and if I believe 23andme I also possess 0.2% of Native American ancestry in the conservative level. I tested with Minimum segment cM to be included in total = 1cm and Minimum threshold size to be included in total=100 snps, and I matched with all the samples I tested, the problem comes from the location of the dna segments of the sample that matched with me. For example, according to 23andme, my dna segments that are native american are located on 3 of my chromosomes, and if I add my dna segments of East Asian origin, on 7 chromosomes in all. But my results showed that I share 111 dna segments located on 21 of my chromosomes with Clovis-Anzick, 69 of which are located on chromosomes in which I have no segment of Native American dna or Asian, worse Still, some of these segments are on 3 of my chromosomes that are entirely African if I believe 23andme. I noted almost the same with the Paleo-Eskimo sample. I can also take as an example a European sample, that of LBK, with which I share 175 segments of dna on 22 chromosomes, of which 11 of these segments are on 4 completely African chromosomes if I believe 23andme, then how Explain this?

I would add, when I took the sample from Altai’s neanderthal, and analyzed it with ”Admixture (heritage)”, I got the result that the sample was predominantly from sub-Saharan Africa, Makes no sense, knowing that according to the geneticists, it is only among Sub-Saharan Africans that no trace of neanderthal DNA can be found. So all those results make me confuse, and i don’t know how to explain it.

You may be setting the thresholds for the ancient matches too low and picking up sections that match simply by chance. Otherwise, I don’t know. Each ethnicity predictor uses it’s own data base, it’s own algorithm and there is no way to correlate them. You are right to be confused. I can’t help you without seeing your results and doing the comparisons, and even if I did, I don’t know that there is any explanation other than the technology as utilized by different people/companies simply doesn’t agree.

You can’t mix comparisons to ancient and modern populations and with a 1 cM threshold, you will match everyone on earth. You may want to look at the discussions on Anthrogenica.com where these topics are discussed in detail and, as a bonus for you, there is a section in French as well (http://www.anthrogenica.com/forumdisplay.php?162-French), although I would say your English is nothing to be ashamed of.

You are right Roberta, that’s exactly what other people have told me: that i setting the thresholds for the ancient matches too low, and indeed when I increased the thresholds I no longer matched with these Samples.
Regarding the bizarre results I had with admixture (heritage) for some of these old samples, as you are told, some of my friends said it’s probably due to the technology employed, or the reference population panel used.

Thank you for the compliment about my English Suzanne, and you’re right with a 1 cm threshold, and 100 SNP threshold I actually match very well with all contemporary people with whom I compared myself. I would also like to thank you for referring me to the site of Anthrogenica.com that I did not know before.

According to this, we have common ancestors.
Comparing Kit A548806 (*Southerngal Kiwi) [Migration – F2 – A] and NQ4782875 (Debbie Lapeyrouse) [MyHeritage V2]
Segment threshold size will be adjusted dynamically between 200 and 400 SNPs
Minimum segment cM to be included in total = 5.0 cM
Mismatch-bunching Limit will be adjusted dynamically to 60 percent of the segment threshold size for any given segment.
Largest segment = 5.2 cM
Total Half-Match segments (HIR) = 5.2 cM (0.144 Pct)
Estimated number of generations to MRCA = 7.7
1 shared segments found for this comparison.
393137 SNPs used for this comparison.
52.047 Pct SNPs are full identical

And I have a paper trail to one of my several lines of Native Americans as well as DNA confirmation. It would be interesting to determine who our common ancestors 7-8 generations back were.

I have compared my kit M358747 to yours, Montana boy, Kentacky and several ancient european remains with gedmatch tool 3D chromosome browser at minimum 3 cM. We have no segments longer than 3 cM with ancient native americans. However the most of iberians I tested (0% native american) have many small segments between 1-3 cM shared with Clovis boy and absolutely nothing with iberian mesolithic la Brana-Leon F999915. Many west europeans have a deep ancient paleo-siberian herency that connects to F999919 Montana.

Sorry, I wanna write Kennewick instead of Kentacky (F999970). First, run another gedmatch tool “archaic dna matches”. Change to 2 cM minimum up and you will see all archaic remains you are related. Then, fill in cases (3D tool) all your archaic relatives and change to minimum 3 cM. You will see Loshbour F999918 and LBK F999916 (archaic western europeans) related to Clovis Child and paleo-Siberian Ust-Ishim F999935.

This is all so interesting, thank you for your continued research/information. I’m fairly new to the DNA world, as I found out I was adopted just a few years ago. I ran my compare to F999919 and matched at Chromosome 6 and 13: 7.4 cM; 1,055 (for Chr 6) and 574 for Chr 13; estimated number of generations to MRCA = 7.0. Minimum threshold was set to 500 SNPs. I enjoy your blog and emails, thank you!

Hi,
My heritage is Creole on my father’s side and I match the Clovis sample at 293cM’s with greater than 200 SNP’s. You mentioned that you have Acadian Native ancestry, so I’m wondering if your Rochette family might possibly be the Rachal family? They were quite prominent in Louisiana and many people of Acadian and/or Creole ancestry include at least one Rachal ancestor in their tree. My GEDMatch number is A524988. Also, just curious if you have any idea how Melanesian ancestry might end up in my Creole line?
Thanks!
Cindy

“Lore” Acadian? Isn’t it interesting that I, who has LEGITIMATE Acadian ancestry for my ancestors NEVER left, has never heard of anyone by the name of “Lore”? Nor does “Lore” show up in the any of the genetic matches. Nowhere is there someone by the name Lore.

So maybe you can do me a favour and name some of these so-called Acadians you match up with. Just surnames would do even. I bet you think French names = Acadians. Forgetting the very simple fact that French were to be found from Manitoba down through the US and back up through to Vermont.

And Bernard Lord, an Acadian, was the premier of the province of New Brunswick at the beginning of the century. The name is not as common to the ears of Americans as Richard or Thibodeau also present in Louisiana, but Acadian nonetheless.
My Acadian ancestors included names such as Allain, Bergereau, Dupuis, Gautier, Landry, Bourg (became Bourque). Would you recognize those?

Total novice, but with the Archaic match, at 0.5 cM and 50 SNPs I match every one of the samples: is this normal? Next, at 1 cM and 100 SNPs I still match almost all except for Altai N. and Denisova. At 2 cM and 200 SNPs the matches have almost all dropped of, but still connected to Clovis, Montana. At 5cM and 500 SNPs all have dropped out except for loschbour, Lux.
Interesting, but confusing.

Hi, Roberta… just saw this older blog! I performed the same tests as you, with my mom and my brother. We three share small Anzick matches (a little over 2 cMs averaging between 200-300 SNPs) on chromosome 5 and 6, and I matched three of her cousins to that same segment on chromosome 6 as well. I haven’t found MRCA for one of the cousins yet, and the other two cousins don’t share a common ancestor with each other… I think. The two families they descend from seem to have married each other a LOT. In fact, one prevailing theory for one couple in the family is that a man married his father’s half-sister. Truly hope we’ve got that one wrong – ick.